Italian prosecutors have controversially invited two high-ranking Sudanese officials to Sicily to testify in the case against a suspected human trafficker who appears to be the victim of mistaken identity.

Magistrates in the case are relying on testimony from the members of the feared secret police in Sudan, which is ruled by Omar Hassan al-Bashir, who has been charged with war crimes.

The pair were allegedly part of a joint operation between Bashir’s regime, the Italian police and the British National Crime Agency responsible for the 2016 arrest in Khartoum of a 35-year-old Eritrean who they alleged was Medhanie Yehdego Mered. Known as “the General”, he was suspected of being one of the world’s most sought-after human traffickers.

But since prosecutors in Palermo announced the arrest, serious doubts have been raised about the man’s identity.

A documentary last year by the Swedish broadcaster SVT in collaboration with the Guardian concluded that Mered was “living it up” in Uganda, while the suspect, a refugee whose name is Medhanie Tesfamariam Berhe, faced up to 15 years in prison.

DNA samples taken from Mered’s three-year-old son and from Berhe’s mother also suggest it is a case of mistaken identity.

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Who is Medhanie Yehdego Mered, ‘the General’? – video profile

Although prosecutors have been unable to provide any witnesses to testify against him, they insist the man in custody is the real trafficker.

To prove their case, they asked a judge to admit the testimony of the two Sudanese police officials who allegedly participated in the man’s arrest and torture.

On Monday a judge in the Palermo criminal court accepted the prosecutors’ request despite opposition from Berhe’s lawyer, Michele Calantropo, who warned of the “grave ethical question” that would be raised by their testimony.

“The Sudanese police are considered the armed force of a cold-blooded dictator who now has two international arrest warrants in his name,” Calantropo told the Guardian. “Migrants’ stories have been steadfast and unsettling on this point. And now in Palermo his officials are being summoned as witnesses.”

Bashir has ruled Sudan since 1989, and in March 2009 became the first sitting president to be indicted by the international criminal court (ICC) for allegedly “directing a campaign of mass murder, rape and pillage against civilians in Darfur”, where rebels have been fighting the government since 2003.

In July 2010, the court issued a second warrant containing three separate counts of genocide.

In his written statement in favour of acknowledging the prosecutors’ request, the judge wrote that “the fact that in 2009 the ICC issued an arrest warrant in the Sudanese president’s name is irrelevant and does not imply that its effects can be extended to all subjects who work for the Sudanese government, insofar as the Sudanese government has cooperated – and continues to cooperate – with international police forces.”

Amnesty International said the judge’s decision was unacceptable for a democratic country.

“Any type of judicial collaboration between Italy and the Sudanese police is morally unacceptable,” said Riccardo Noury, a spokesman for Amnesty in Italy. “Considering they’ve invited members of his police force, why don’t they extend their invitation to Bashir himself? They might do the ICC a favour and turn him over to the judicial authorities.”

The Belgian government was criticised last year after it invited Sudanese officials to Brussels to identify migrants and provide documents for their forced return. Opposition politicians and aid groups accused the government of collaborating with the regime.

Last year EU leaders backed plans to tighten the EU’s external border, give more money to countries such as Turkey and Morocco to help prevent migrants leaving for Europe, and set up processing centres in countries such as Libya and Niger.

In an email sent to the Sicilian prosecutors in January 2016 and obtained by the Guardian, the British NCA representative in north Africa, Roy Godding, wrote that the “NCA is establishing new relationships with the local police in Sudan”.

Amjed Farid, a member of the Sudan Doctors Syndicate, a professional association, and the spokesperson for the Sudan Change Now political movement, said: “Italy, with the backing of the EU, is betraying itself and its objectives by dealing and cooperating with the cause of the migration. The Sudanese regime is one big cause of migration and flight from Africa because of its brutality and mismanagement and tyranny.”

The NCA and Italian prosecutors declined to comment “until the conclusion of the court case”.

On Monday, the court in Palermo rejected the testimony of a witness who had seen the real trafficker and said he knew his network.